omicverse.single.pathway_aucell_enrichment

omicverse.single.pathway_aucell_enrichment(adata, pathways_dict, AUC_threshold=0.01, seed=42, num_workers=1, gene_overlap_threshold=0.8)[source]

Enrich cell annotations with pathway activity scores using the AUC-ell method.

Parameters:

  • adata (anndata.AnnData) – AnnData containing expression matrix.

  • pathways_dict (dict) – Mapping from pathway name to list of genes.

  • AUC_threshold (float) – AUCell rank threshold percentile.

  • seed (int) – Random seed for AUCell backend.

  • num_workers (int) – Number of workers used in AUCell computation.

  • gene_overlap_threshold (float) – Minimum fraction of pathway genes present in adata.var_names.

Returns:

AnnData whose X stores pathway AUCell activity matrix.

Return type:

anndata.AnnData